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IM program for fitting the Isolation w/ Migration model using a MCMC method : IM is a program, written by Jody Hey and Rasmus Nielsen, for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations

Author(s)

Hey and Nielsen


Version

1


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IMa program for fitting the Isolation w/ Migration model using a MCMC method : IMa is a program, written by Jody Hey and Rasmus Nielsen, for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations

Author(s)

Hey and Nielsen


Version

2.0


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iRAP is a flexible computational pipeline for RNA-seq that integrates many existing tools for filtering and mapping reads, quantifying expression and testing for differential expression. It is aimed at a broad group of users with basic bioinformatics training and requires little experience with the command line but also provides more advanced users with the ability to customise the options used by their chosen tools.

Author(s)

Unknown


Version

1


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This version processes a de novo assembly to generate a fasta reference file and a gtf file.

iRAP is a flexible computational pipeline for RNA-seq that integrates many existing tools for filtering and mapping reads, quantifying expression and testing for differential expression. It is aimed at a broad group of users with basic bioinformatics training and requires little experience with the command line but also provides more advanced users with the ability to customise the options used by their chosen tools.

Author(s)

Unknown


Version

1


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LS TEST

Tool

 

This is a simple test of Pise

Author(s)

Julien V, Jimmy L


Version

1


Subsections

Tool


Tags

Apps


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MACSE

Alignment

 

Citation: Ranwez V, Harispe S, Delsuc F, Douzery EJP (2011) MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons. PLoS ONE 6(9): e22594. doi:10.1371/journal.pone.0022594

corresponding author: vincent.ranwez@supagro.inra.fr

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment.

We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.

MACSE is distributed as an open-source java file executable with freely available source code and can be used via this web interface.

Online Tool version : 2.01b

This Source code of MACSE can be downloaded, using the svn facilities of redmine with the following command line and "guest" as login and password: svn checkout http://kimura.univ-montp2.fr/svn/macse
project web page
N.B.: online access to this tool is limited (details here)

Check latest release, MACSE version (2.01b). executable (jar file) with source code here .

corresponding author: vincent.ranwez@supagro.inra.fr

Author(s)

Vincent RANWEZ, Sebastien HARISPE, Frederic DELSUC, Emmanuel J. P. DOUZERY


Version

2.01b


Subsections

Alignment


MACSE V0.9

Alignment

 

Citation: Ranwez V, Harispe S, Delsuc F, Douzery EJP (2011) MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons. PLoS ONE 6(9): e22594. doi:10.1371/journal.pone.0022594

corresponding author: vincent.ranwez@supagro.inra.fr

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment.

We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.

MACSE is distributed as an open-source java file executable with freely available source code and can be used via this web interface.

Online Tool version : 0.9b1

This Source code of MACSE can be downloaded, using the svn facilities of redmine with the following command line and "guest" as login and password: svn checkout http://kimura.univ-montp2.fr/svn/macse
project web page
N.B.: online access to this tool is limited (details here)

Check latest release, MACSE version (1.01b). executable (jar file) with source code here .

corresponding author: vincent.ranwez@supagro.inra.fr

Author(s)

Vincent RANWEZ, Sebastien HARISPE, Frederic DELSUC, Emmanuel J. P. DOUZERY


Version

0.9b1


Subsections

Alignment


MACSE V1

Alignment

 

Citation: Ranwez V, Harispe S, Delsuc F, Douzery EJP (2011) MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons. PLoS ONE 6(9): e22594. doi:10.1371/journal.pone.0022594

corresponding author: vincent.ranwez@supagro.inra.fr

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment.

We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.

MACSE is distributed as an open-source java file executable with freely available source code and can be used via this web interface.

Online Tool version : 1.01b

This Source code of MACSE can be downloaded, using the svn facilities of redmine with the following command line and "guest" as login and password: svn checkout http://kimura.univ-montp2.fr/svn/macse
project web page
N.B.: online access to this tool is limited (details here)

Check latest release, MACSE version (1.01b). executable (jar file) with source code here .

corresponding author: vincent.ranwez@supagro.inra.fr

Author(s)

Vincent RANWEZ, Sebastien HARISPE, Frederic DELSUC, Emmanuel J. P. DOUZERY


Version

1.01b


Subsections

Alignment


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MACSE_v2

Alignment

 

Citation: Ranwez V, Harispe S, Delsuc F, Douzery EJP (2011) MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons. PLoS ONE 6(9): e22594. doi:10.1371/journal.pone.0022594

corresponding author: vincent.ranwez@supagro.inra.fr

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment.

We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.

MACSE is distributed as an open-source java file executable with freely available source code and can be used via this web interface.

Online Tool version : 2.01b

This Source code of MACSE can be downloaded, using the svn facilities of redmine with the following command line and "guest" as login and password: svn checkout http://kimura.univ-montp2.fr/svn/macse
project web page
N.B.: online access to this tool is limited (details here)

Check latest release, MACSE version (2.01b). executable (jar file) with source code here .

corresponding author: vincent.ranwez@supagro.inra.fr

Author(s)

Vincent RANWEZ, Sebastien HARISPE, Frederic DELSUC, Emmanuel J. P. DOUZERY


Version

2.01b


Subsections

Alignment


MAFFT

Alignment

 

MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of

Author(s)

Kazutaka Katoh


Version

6.814b


Subsections

Alignment


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Magic-BLAST is a new tool for mapping large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.

Author(s)

Unknown


Version

1.1


Subsections

Tool - Blast


Tags

RNA-seq - Apps


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Used in order to perform a Mantel test based on two distance matrix. The number of permutations can be specified. An HTML file containing a graphical representation of the statistic Z distribution is generated.

Author(s)

Sara Jaillet & Khalid Belkhir


Version

1


Subsections

Tool


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Megablast

Alignment

 

Mega BLAST uses a greedy algorithm [1] for the nucleotide sequence alignment search. This program is optimized for aligning sequences that differ slightly as a result of sequencing or other similar "errors". When larger word size is used (see explanation below), it is up to 10 times faster than more common sequence similarity programs. Mega BLAST is also able to efficiently handle much longer DNA sequences than the blastn program of traditional BLAST algorithm.

Author(s)

NCBI -Tao Tao


Version

1


Subsections

Alignment - Blast


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Build database giving a sequence file in order to blast query sequences on it using magablast. Treatment performed using formatDB and megablast (8 cores).

Author(s)

Altschul, Madden, Schaeffer, Zhang, Miller, Lipman ... [wrapper : MBB development team]


Version

1


Subsections

Blast


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This pipeline will assemble paired-end reads with Megahit. The resulting contigs are then mapped on NCBI refseq mitochondrion database to filter mitochondrial sequences.

Author(s)

M. Massaviol & K. Belkhir


Version

1


Subsections

Alignment - Assembler


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